Beefed up national security laws will streamline the flow of defence technology between Australia, America and Britain but there could be repercussions for the science sector.
Listed technology will not be able to be shared with foreigners unless an export licence is approved, if draft trade control laws pass.
Three new criminal offences will be created to stop the technology falling into foreign hands.
The US and UK will be exempt from needing a licence to encourage the flow of technology through the AUKUS alliance between the three nations.
Chief Executive of the Australian Academy of Science Anna-Maria Arabia said it was difficult to know if more would be lost than gained for the scientific community.
Almost all of Australia's knowledge base wasn't generated onshore, she said.
"There will be ramifications for the research sector - I would go as far as to say there might be quite a shake up of the way the research system architecture operates," she told ABC TV on Tuesday.
It was important the national security and research communities communicated with each other to make sure any changes to technology sharing were proportional, Ms Arabia said.
It would affect AI, quantum, cybersecurity and semiconductor research, she said.
There was also a risk that research partners like New Zealand, Germany or France may view the extra bureaucracy as too much of a burden and "not pursue collaborations which are within Australia's interest".
"There will be missed opportunities in terms of collaborations ... the research community in Australia collaborates with really everyone in the world," she said.
Defence Minister Richard Marles said the new laws would be "game-changing reforms for Australia's defence industry".
"The Albanese government is once again taking another decisive step forward in delivering nuclear-powered submarines and further technology sharing under the AUKUS framework," he said in a statement.
The US Congress is also considering legislation to make it easier to export military technology to Australia.
